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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeDB_2.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BgeeDB.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.30.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BgeeDB’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BgeeDB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadTopAnatData
> ### Title: Retrieve data from Bgee to perform GO-like enrichment of
> ###   anatomical terms, mapped to genes by expression patterns.
> ### Aliases: loadTopAnatData
> 
> ### ** Examples
> 
> {
+   bgee <- Bgee$new(species = "Danio_rerio", dataType = "rna_seq")
+   myTopAnatData <- loadTopAnatData(bgee)
+ }

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /Users/biocbuild/bbs-3.19-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: 431802c999f431ba5dc7841927bb2bbbd8362470b8b540931cf56edbef028784cd78596964ae08e00d0c4c75e896a7a32cf71cb7a87b7878dd1e9550b2d12f3a

NOTE: an organ relationships file was found in the download directory /Users/biocbuild/bbs-3.19-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_0. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /Users/biocbuild/bbs-3.19-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_0. Data will not be redownloaded.

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://www.bgee.org/bgee15_0/api/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=7955&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=431802c999f431ba5dc7841927bb2bbbd8362470b8b540931cf56edbef028784cd78596964ae08e00d0c4c75e896a7a32cf71cb7a87b7878dd1e9550b2d12f3a&source=BgeeDB_R_package&source_version=2.30.0&data_type=RNA_SEQ&data_qual=SILVER)
   Submitting URL to Bgee webservice (can be long)
Warning in download.file(url = url, destfile = destfile, quiet = quiet) :
  URL 'https://archives.bgee.org/api-15-0/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=7955&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=431802c999f431ba5dc7841927bb2bbbd8362470b8b540931cf56edbef028784cd78596964ae08e00d0c4c75e896a7a32cf71cb7a87b7878dd1e9550b2d12f3a&source=BgeeDB_R_package&source_version=2.30.0&data_type=RNA_SEQ&data_qual=SILVER': status was 'Failure when receiving data from the peer'
Error in download.file(url = url, destfile = destfile, quiet = quiet) : 
  download from 'https://www.bgee.org/bgee15_0/api/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=7955&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=431802c999f431ba5dc7841927bb2bbbd8362470b8b540931cf56edbef028784cd78596964ae08e00d0c4c75e896a7a32cf71cb7a87b7878dd1e9550b2d12f3a&source=BgeeDB_R_package&source_version=2.30.0&data_type=RNA_SEQ&data_qual=SILVER' failed
Calls: loadTopAnatData -> bgee_download_file -> download.file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.